4CDV

Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 100K


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SULFATE, HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5852.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.281α = 90
b = 53.281β = 90
c = 180.751γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.1746.1950.0517.15.749558
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.171.2469.70.12.62.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2YLI1.1746.1446928250094.950.140610.139580.15998RANDOM9.939
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.3-0.3-0.30.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.452
r_sphericity_free26.754
r_dihedral_angle_4_deg20.364
r_rigid_bond_restr15.815
r_dihedral_angle_3_deg13.23
r_sphericity_bonded8.003
r_dihedral_angle_1_deg5.062
r_angle_refined_deg2.074
r_angle_other_deg1.254
r_scbond_it1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.452
r_sphericity_free26.754
r_dihedral_angle_4_deg20.364
r_rigid_bond_restr15.815
r_dihedral_angle_3_deg13.23
r_sphericity_bonded8.003
r_dihedral_angle_1_deg5.062
r_angle_refined_deg2.074
r_angle_other_deg1.254
r_scbond_it1.2
r_mcangle_it1.064
r_mcbond_it0.877
r_mcbond_other0.861
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms949
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling